r259: change an assertion failure to warning

When bonus score is too high, the assert doesn't work.

align.c

@@ -78,7 +78,7 @@ static int32_t mp_align_seq(void *km, const mp_mapopt_t *opt, const ns_opt_t *ns
 	}
 }
 
-static void mp_extra_cal(mp_reg1_t *r, const mp_mapopt_t *opt, const uint8_t *nt, int32_t l_nt, const char *aa, int32_t qlen)
+static void mp_extra_cal(mp_reg1_t *r, const mp_mapopt_t *opt, const uint8_t *nt, int32_t l_nt, const char *aa, int32_t qlen, int32_t has_spsc)
 {
 	int32_t k, i, j, l, nl = 0, al = 0, ft, n_intron, has_stop;
 	int32_t blen0, n_iden0, phase0, qs0, n_fs0, n_stop0, score0;
@@ -186,13 +186,12 @@ static void mp_extra_cal(mp_reg1_t *r, const mp_mapopt_t *opt, const uint8_t *nt
 	}
 	// check errors
 	if (nl != r->ve - r->vs || al != r->qe - r->qs) {
-		fprintf(stderr, "BUG! %d == %d? %d == %d? ", nl, (int)(r->ve - r->vs), al, r->qe - r->qs);
-		for (k = 0; k < e->n_cigar; ++k)
-			fprintf(stderr, "%d%c", e->cigar[k]>>4, NS_CIGAR_STR[e->cigar[k]&0xf]);
-		fputc('\n', stderr);
+		if (mp_verbose >= 2)
+			fprintf(stderr, "Warning: unknown issue with --spsc (%d!=%d or %d!=%d)\n", nl, (int)(r->ve - r->vs), al, r->qe - r->qs);
+		free(r->p); free(r->feat);
+		r->p = 0, r->feat = 0;
 	}
-	assert(nl == r->ve - r->vs);
-	assert(al == r->qe - r->qs);
+	assert(has_spsc == 1 || (nl == r->ve - r->vs && al == r->qe - r->qs));
 }
 
 static void mp_extra_gen(void *km, mp_reg1_t *r, mp_cigar_t *cigar, int32_t score)
@@ -329,7 +328,7 @@ void mp_align(void *km, const mp_mapopt_t *opt, const mp_idx_t *mi, int32_t len,
 	mp_extra_gen(km, r, &cigar, score);
 	r->p->dist_stop  = mp_extra_stop(r, nt, as, ae);
 	r->p->dist_start = mp_extra_start(r, nt, as, ae);
-	mp_extra_cal(r, opt, &nt[r->vs - as], l_nt - (r->vs - as), &aa[r->qs], len);
+	mp_extra_cal(r, opt, &nt[r->vs - as], l_nt - (r->vs - as), &aa[r->qs], len, mi->nt->spsc != 0);
 	if (ss) kfree(km, ss);
 	kfree(km, nt);
 }

main.c

@@ -190,7 +190,7 @@ int main(int argc, char *argv[])
 	if (set_I && !set_G) mp_mapopt_set_max_intron(&mo, mi->nt->l_seq);
 	if (mp_verbose >= 3) mp_idx_print_stat(mi, mo.max_occ);
 	if (fn_idx != 0) mp_idx_dump(fn_idx, mi);
-	if (fn_spsc != 0) mp_ntseq_read_spsc(mi->nt, fn_spsc);
+	if (fn_spsc != 0) mp_ntseq_read_spsc(mi->nt, fn_spsc, mo.io - mo.go);
 	for (i = o.ind + 1; i < argc; ++i) {
 		int32_t res = mp_map_file(mi, argv[i], &mo, n_threads);
 		if (res != 0) {

miniprot.h

@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#define MP_VERSION "0.13-r258-dirty"
+#define MP_VERSION "0.13-r259-dirty"
 
 #define MP_F_NO_SPLICE    0x1
 #define MP_F_NO_ALIGN     0x2
@@ -162,7 +162,7 @@ void mp_idx_destroy(mp_idx_t *mi);
 int mp_idx_dump(const char *fn, const mp_idx_t *mi);
 mp_idx_t *mp_idx_restore(const char *fn);
 void mp_idx_print_stat(const mp_idx_t *mi, int32_t max_occ);
-int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn);
+int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn, int32_t max_sc);
 
 int32_t mp_map_file(const mp_idx_t *idx, const char *fn, const mp_mapopt_t *opt, int n_threads);
 

ntseq.c

@@ -232,9 +232,7 @@ int32_t mp_ntseq_name2id(const mp_ntdb_t *nt, const char *name)
 	return k == kh_end(h)? -1 : kh_val(h, k);
 }
 
-#define MP_MAX_SPSC 30
-
-int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn)
+int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn, int32_t max_sc)
 {
 	gzFile fp;
 	kstring_t str = {0,0,0};
@@ -274,7 +272,7 @@ int32_t mp_ntseq_read_spsc(mp_ntdb_t *nt, const char *fn)
 		}
 		if (i < 4) continue; // not enough fields
 		if (score <= 0) continue;
-		if (score > MP_MAX_SPSC) score = MP_MAX_SPSC;
+		if (score > max_sc) score = max_sc;
 		cid = mp_ntseq_name2id(nt, name);
 		if (cid < 0 || type < 0 || strand == 0 || pos < 0) continue; // FIXME: give a warning!
 		s = &nt->spsc[cid << 1 | (strand > 0? 0 : 1)];